SMTL ID : 8qmo.1

Cryo-EM structure of the benzo[a]pyrene-bound Hsp90-XAP2-AHR complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

2 x MOO: MOLYBDATE ION(Non-covalent)

MOO.1: 10 residues within 4Å: Chain A: E.48, G.133, Q.134, F.135, G.136, V.137, G.138, R.398 Ligands: ADP.2, MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.134, A:F.135, A:G.136, A:V.137, A:G.138, A:R.398, A:R.398 MOO.4: 10 residues within 4Å: Chain B: E.48, G.133, Q.134, F.135, G.136, V.137, G.138, R.398 Ligands: ADP.5, MG.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.134, B:F.135, B:G.136, B:V.137, B:G.138, B:R.398, B:R.398

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 24 residues within 4Å: Chain A: N.52, A.53, A.56, K.59, D.94, I.97, G.98, M.99, N.107, L.108, K.113, S.114, G.115, T.116, G.133, Q.134, F.135, G.136, V.137, G.138, F.139, T.185 Ligands: MOO.1, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.52, A:K.59, A:D.94, A:N.107, A:S.114, A:S.114, A:G.115, A:T.116, A:T.116, A:G.133, A:F.135, A:G.136, A:V.137, A:G.138, A:F.139, A:T.185 ADP.5: 25 residues within 4Å: Chain B: N.52, A.53, A.56, K.59, D.94, I.97, G.98, M.99, N.107, L.108, K.113, S.114, G.115, T.116, G.133, Q.134, F.135, G.136, V.137, G.138, F.139, T.185, V.187 Ligands: MOO.4, MG.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:N.52, B:N.52, B:K.59, B:D.94, B:N.107, B:S.114, B:G.115, B:T.116, B:T.116, B:G.133, B:F.135, B:G.136, B:G.138, B:F.139, B:T.185

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: E.48, N.52, G.138 Ligands: MOO.1, ADP.2 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain B: E.48, N.52, G.138 Ligands: MOO.4, ADP.5 No protein-ligand interaction detected (PLIP)

1 x W62: benzo[a]pyrene(Non-covalent)

W62.7: 14 residues within 4Å: Chain D: H.293, F.297, G.323, Y.324, F.326, I.327, C.335, S.338, H.339, I.351, F.353, L.355, S.367, V.383 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:F.297, D:F.297, D:F.297, D:F.297, D:F.326, D:I.327, D:H.339, D:I.351, D:F.353, D:L.355, D:V.383 pi-Stacking: D:H.293, D:F.297, D:F.297, D:F.353

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwong, H.S. et al., Structural Insights into the Activation of Human Aryl Hydrocarbon Receptor by the Environmental Contaminant Benzo[a]pyrene and Structurally Related Compounds. J.Mol.Biol. (2024)

Release Date

2024-01-10

Peptides

Heat shock protein HSP 90-beta: AB
AH receptor-interacting protein: C
Aryl hydrocarbon receptor: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Heat shock protein HSP 90-beta

AH receptor-interacting protein

Aryl hydrocarbon receptor

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